I've got both expansions, and I'm running a game (4-6 players) this weekend.  All of my players are sharp enough to pick things up quickly, so I'm confident I have the whole field of options available to choose from, and we don't get together often enough to want to "waste" an evening experimenting.  On the other hand, I personally have only experienced the base game and Pegasus, but not Exodus (and let's just assume this inexperience won't be a problem).  So, with the whole field of options available to me, I come to you fine folks for some insight into the rules, options and expansion components that I should and should not include.

I usually try to ask more direct questions when starting a new topic, but that's a bit tricky here.  Generally speaking, could you please provide comments on your experiences with different combinations, and any recommendations or "sweet spot" combinations (even for different player counts) you may have discovered?  I'd like to get a clearer sense of what to expect to design the kind of game we want to play, without having to waste one of our precious, rare gaming evenings fumbling about and experimenting for ourselves!

Let me try to get the ball rolling with some questions, but any advice would be much appreciated!

1. Is there anything in Pegasus that is IMPROVED by additions from Exodus? Like Cylon Leaders? I'd love those Cylon Leaders to be everything they were intended to be, and it would be nice if Treachery actually, you know, did stuff.  In your experience, does Exodus show signs of being playtested and designed with Pegasus in mind, or are they more like two ships passing in the night that managed to avoid a messy collision?
2. What Pegasus/Exodus options are especially harsh on game length? Time-between-turns?  My players are sharp, but they're the antsy sort.  Games can go long if there's action, if turns move quickly and/or if there's plenty to do when it isn't your turn.  But if, say, the Ionian Nebula's Ally cards double the length of each turn, well, I'll probably leave them out.  On the other hand, the Cylon Fleet Option looks like it's designed to keep things crackling whoever's turn it is.
3. Advice on Upping the Paranoia? This may just be fallout from our 6-player Pegasus experience with a sympathetic Cylon Leader, which basically cost us an unrevealed Cylon and replaced him with a character that everyone ignored.  I'm thinking the Conflicted Loyalties option is the most obvious thing to add; it seems simple, and is clearly designed to do just this.  Any take on whether to include both Final Five and Personal Goal, or does one work better than the other?
4. Cylon Leader vs. Sympathetic Cylon vs. Sympathizer? Assuming a 4 or 6 player game, any advice on which to go with?  I loathe the Sympathizer because it truly sucks for whoever gets it and encourages silly pre-Sleeper metagaming, and I'm a stickler for flavor.  On the other hand, I'm doubtful that a Sympathetic Cylon Leader will ever be worthy of replacing an unrevealed Cylon (you think this would have come up around the design table...).  So I'm leaning towards the Sympathetic Cylon card as a midway between both worlds, but damn, I'd REALLY like to make Cylon Leaders exciting and paranoia-inducing.
5. What about diluting decks? I know there were complaints that merely shuffling the Pegasus crisis cards into the main Crisis deck made those Pegasus cards few and far between, and I worry that the Exodus crisis cards might cause the same problem.  Same goes for Exodus Skill cards drowning out the Reckless checks and making Treachery even more pointless.
6. General advice on combining Exodus with (or without) Pegasus: I just want to reiterate that I don't have any experience playing Exodus, so any insights you have specifically from playing Exodus that may not be so obvious from a read of the rules would be greatly appreciated!

Okay, I think six is enough!  Thanks for making it this far, and thanks in advance for any advice you take the time to provide, it's much appreciated!

PS (and I'll edit this as my plans change): As of this initial post, I'm considering running

• All three expansions, with the Kobol objective.
• Pegasus: No Cylon Leaders (*sob*), but a Sympathetic Cylon card, if necessary, that might create one.  No New Caprica objective.
• Exodus: Conflicted Loyalties and Cylon Fleet options.  No Ionian Nebula option.

I haven't mixed Exodus and Pegasus, just played with one or the other, so can't really answer most of your questions. But I can hopefully help with this:

1. Advice on Upping the Paranoia? This may just be fallout from our 6-player Pegasus experience with a sympathetic Cylon Leader, which basically cost us an unrevealed Cylon and replaced him with a character that everyone ignored.  I'm thinking the Conflicted Loyalties option is the most obvious thing to add; it seems simple, and is clearly designed to do just this.  Any take on whether to include both Final Five and Personal Goal, or does one work better than the other?

The Final Five cards have zero effect unless the players are looking at loyalty cards a lot. If your goal is to up the paranoia, leave them out. If you want tons of paranoia, leave out the blank "You are not a cylon" cards and only use the ones with Personal goals. you may want to start with increased resources if you're doing this though, as there will be some guaranteed losses should the humans survive to the end.

Err, I realize I mangled some of the "Cylon Leader replacing an unrevealed Cylon" rules in the above post; I've honestly gone and confused myself, as I know I played a Sympathetic Cylon, I know we had more than four players, and I can only remember one other Cylon player.  I'm thinking I just forgot about the second Cylon, and conflated complaints I read about the 5-player game replacing an unrevealed Cylon with a revealed Cylon Leader.  Also, I can't seem to find the edit button to fix my mistake, which would also make all those promises about editing said post a lie. 

I guess I'm just a terrible person.

James McMurray said:

Ah, I had assumed that Exodus would include Crisis/Quorum/etc. cards that would increase the frequency of checking others' Loyalty cards.  Is this the case, or did they print five cards just to screw over Gaius Baltar? ;-)

Not sure. I haven't read all of the cards (I like them to be a surprise). I do know that there are several ways besides just Baltar to look at loyalty cards, including Crisis cards and Quorum cards. And that some of them came before Exodus.

The edit button is at the top of the post, but the forum software takes it away after a certain amount of time (not sure how long).

One thing I can say is that if you mix them, you should probably use the Ionian Nebula instead of New Caprica. NC's massive shift from the base game can be a pain for new players, even really smart ones. That and, IMO, the Nebula fits a lot better with the BSG theme than NC did.

Given the amount of time Exodus has now been out, I would think FFG would have posted rules on how to combine various aspects of it with Pegasus.  I can understand how this would be difficult, especially considering the fact that many groups use bits and pieces of each expansion (screw New Caprica, I'm sorry, but I'll say that every chance I get) but some sort of guidelines or something would be good; everyone is playing it differently right now.  Its going to get even worse if a 3rd expansion does come out.
Anyone else who has played entirely too many games of this think we should start a thread about how to combine them without making the game length too excessive?  I realize there are various answers scattered through several threads, it might be nice to put it all in one place - maybe we can figure out the most balanced answer.  In fact, I'm gonna start it here.

Thanks for your advice, all!  I've managed to play three games of BSG since I wrote the OP, and made an important realization:  It doesn't matter how smart you are when it comes to adding expansions; until you know the base game like the back of your hand, there's just too much to take in.

So, I made only a few modifications to the base game, and am now running a sort of "BasePlus" game until we're ready to add parts of Pegasus/Exodus:

• The "real" basics:  New Investigative Committee and Cylon locations.
• Sympathetic Cylon Loyalty Card replaces Sympathizer (Infiltration & Sympathetic Agendas along for the ride)
• Exodus' two "You Are A Cylon" Loyalty Cards (jump prep -2, and centurion on Galactica)
• "Scar" and "Dogfights" Crisis Cards for more Cylon attacks, and "Mining Asteroid" Destination from Pegasus (the latter replacing a "Deep Space" Destination card)
• Exchanged some of those quadruplicates in the Crisis deck (Food/Water Shortages) for similar Crisis Cards from Pegasus/Exodus, for greater variety since we like to read the flavor text (this re-balanced the jump icon ratio, which was changed after adding the two Cylon Attacks above)
• Added just a few of the more interesting Quorum Cards (The Oracle is the only one I can think of now)
• Added all of the Super Crisis Cards that didn't directly reference mechanics we weren't using, like execution or Treachery

I left out a lot of things I could have included, because I want something to encourage playing those expansions when we're ready, even if all I have to lure them in is new Crisis and Skill Cards!